def test_dicom_store_instance(self):
# Store DICOM files to a empty DICOM store from a GCS bucket,
# then check if the store metadata match.
input_dict = {}
input_dict['project_id'] = self.project
input_dict['region'] = REGION
input_dict['dataset_id'] = DATA_SET_ID
input_dict['dicom_store_id'] = self.temp_dicom_store
input_dict['search_type'] = "instances"
expected_dict = {}
expected_dict['result'] = self.expected_output_metadata
expected_dict['status'] = 200
expected_dict['input'] = input_dict
expected_dict['success'] = True
with TestPipeline() as p:
gcs_path = DICOM_FILES_PATH + "/*"
results = (p
| fileio.MatchFiles(gcs_path)
| fileio.ReadMatches()
| UploadToDicomStore(input_dict, 'fileio')
| beam.Map(lambda x: x['success']))
assert_that(results, equal_to([True] * NUM_INSTANCE))
with TestPipeline() as p:
results = (p | beam.Create([input_dict]) | DicomSearch())
assert_that(results, equal_to([expected_dict]))
def test_dicom_store_instance_from_gcs(self):
# Store DICOM files to a empty DICOM store from a GCS bucket,
# then check if the store metadata match.
input_dict_store = {}
input_dict_store['project_id'] = self.project
input_dict_store['region'] = REGION
input_dict_store['dataset_id'] = DATA_SET_ID
input_dict_store['dicom_store_id'] = self.temp_dicom_store
expected_output = [True] * NUM_INSTANCE
with self.test_pipeline as p:
gcs_path = DICOM_FILES_PATH + "/io_test_files/*"
results = (p
| fileio.MatchFiles(gcs_path)
| fileio.ReadMatches()
| UploadToDicomStore(input_dict_store, 'fileio')
| beam.Map(lambda x: x['success']))
assert_that(results,
equal_to(expected_output),
label='store first assert')
# Check the metadata using client
result, status_code = DicomApiHttpClient().qido_search(
self.project, REGION, DATA_SET_ID, self.temp_dicom_store,
'instances')
self.assertEqual(status_code, 200)
# List comparison based on different version of python
self.assertCountEqual(result, self.expected_output_all_metadata)
def test_store_fileio_file_small_buffer_flush(self, FakeClient):
input_dict = {}
input_dict['project_id'] = "test_project"
input_dict['region'] = "test_region"
input_dict['dataset_id'] = "test_dataset_id"
input_dict['dicom_store_id'] = "test_dicom_store_id"
fc = FakeHttpClient()
FakeClient.return_value = fc
temp_dir = '%s%s' % (self._new_tempdir(), os.sep)
dict_input_1 = {
'PatientName': 'George', 'Age': 23, 'TestResult': 'Negative'
}
str_input_1 = json.dumps(dict_input_1)
self._create_temp_file(dir=temp_dir, content=str_input_1)
dict_input_2 = {'PatientName': 'Peter', 'Age': 54, 'TestResult': 'Positive'}
str_input_2 = json.dumps(dict_input_2)
self._create_temp_file(dir=temp_dir, content=str_input_2)
dict_input_3 = {'PatientName': 'Zen', 'Age': 27, 'TestResult': 'Negative'}
str_input_3 = json.dumps(dict_input_3)
self._create_temp_file(dir=temp_dir, content=str_input_3)
with TestPipeline() as p:
results = (
p
| beam.Create([FileSystems.join(temp_dir, '*')])
| fileio.MatchAll()
| fileio.ReadMatches()
| UploadToDicomStore(input_dict, 'fileio', buffer_size=1)
| beam.Map(lambda x: x['success']))
assert_that(results, equal_to([True] * 3))
self.assertTrue(dict_input_1 in fc.dicom_metadata)
self.assertTrue(dict_input_2 in fc.dicom_metadata)
self.assertTrue(dict_input_3 in fc.dicom_metadata)
def test_store_byte_file_small_buffer_flush(self, FakeClient):
input_dict = {}
input_dict['project_id'] = "test_project"
input_dict['region'] = "test_region"
input_dict['dataset_id'] = "test_dataset_id"
input_dict['dicom_store_id'] = "test_dicom_store_id"
fc = FakeHttpClient()
FakeClient.return_value = fc
dict_input_1 = {
'PatientName': 'George', 'Age': 23, 'TestResult': 'Negative'
}
str_input_1 = json.dumps(dict_input_1)
bytes_input_1 = bytes(str_input_1.encode("utf-8"))
dict_input_2 = {'PatientName': 'Peter', 'Age': 54, 'TestResult': 'Positive'}
str_input_2 = json.dumps(dict_input_2)
bytes_input_2 = bytes(str_input_2.encode("utf-8"))
dict_input_3 = {'PatientName': 'Zen', 'Age': 27, 'TestResult': 'Negative'}
str_input_3 = json.dumps(dict_input_3)
bytes_input_3 = bytes(str_input_3.encode("utf-8"))
with TestPipeline() as p:
results = (
p
| beam.Create([bytes_input_1, bytes_input_2, bytes_input_3])
| UploadToDicomStore(input_dict, 'bytes', buffer_size=1)
| beam.Map(lambda x: x['success']))
assert_that(results, equal_to([True] * 3))
self.assertTrue(dict_input_1 in fc.dicom_metadata)
self.assertTrue(dict_input_2 in fc.dicom_metadata)
self.assertTrue(dict_input_3 in fc.dicom_metadata)
def test_missing_parameters(self, FakeClient):
input_dict = {}
input_dict['project_id'] = "test_project"
input_dict['region'] = "test_region"
expected_invalid_dict = {}
expected_invalid_dict['result'] = []
expected_invalid_dict['status'] = 'Must have dataset_id in the dict.'
expected_invalid_dict['input'] = input_dict
expected_invalid_dict['success'] = False
fc = FakeHttpClient()
FakeClient.return_value = fc
with self.assertRaisesRegex(ValueError,
"Must have dataset_id in the dict."):
p = TestPipeline()
_ = (p | beam.Create(['']) | UploadToDicomStore(input_dict, 'bytes'))
def test_destination_notfound(self, FakeClient):
input_dict = {}
# search instances in a not exist store
input_dict['project_id'] = "wrong_project"
input_dict['region'] = "wrong_region"
input_dict['dataset_id'] = "wrong_dataset_id"
input_dict['dicom_store_id'] = "wrong_dicom_store_id"
expected_invalid_dict = {}
expected_invalid_dict['status'] = 204
expected_invalid_dict['input'] = ''
expected_invalid_dict['success'] = False
fc = FakeHttpClient()
FakeClient.return_value = fc
with TestPipeline() as p:
results = (
p | beam.Create(['']) | UploadToDicomStore(input_dict, 'bytes'))
assert_that(results, equal_to([expected_invalid_dict]))
def test_store_byte_file(self, FakeClient):
input_dict = {}
input_dict['project_id'] = "test_project"
input_dict['region'] = "test_region"
input_dict['dataset_id'] = "test_dataset_id"
input_dict['dicom_store_id'] = "test_dicom_store_id"
fc = FakeHttpClient()
FakeClient.return_value = fc
dict_input = {'PatientName': 'George', 'Age': 23, 'TestResult': 'Negative'}
str_input = json.dumps(dict_input)
bytes_input = bytes(str_input.encode("utf-8"))
with TestPipeline() as p:
results = (
p
| beam.Create([bytes_input])
| UploadToDicomStore(input_dict, 'bytes')
| beam.Map(lambda x: x['success']))
assert_that(results, equal_to([True]))
self.assertTrue(dict_input in fc.dicom_metadata)